It's not just changing the representation in the preview. It's changing the gcode that controls the machine.
For instance, here are sections of gcode from 2 different raft separation settings. The first is with .14mm and the 2nd is with 1mm.
In the first example, layer 7 (the first layer after the raft) is at Z = 2.2473 and layer 8 is at Z = 2.3073. Layer 8 is above layer 7.
In the second example, layer 7 is at Z = 3.1073 and layer 8 is at Z = 2.3073. Layer 8 is below layer 7.
Notice layer 8 Z setting did not change regardless of the separation. Layer separation only affected one layer instead of shifting the whole model.
So layer 7 is the only layer that got the separation applied, and then the nozzle dives back down to the same height for layer 8 regardless of the setting you applied that is supposed to elevate the entire model above the raft. You can effectively never get more separation except for the first layer of the model (layer 7 in this case) and at best, layer 7 didn't stick to the raft quite as badly however the nozzle will basically push layer 7 down to the raft when it does layer 8. This is just really ugly.
Whether or not there is nothing but air under the nozzle allowing layer 7 to fall to the raft is beside the point. It's simply doing the wrong thing in the gcode. The preview is working like a CNC backplot function to show what the generated code will do. With the powerful multi-process and multi model capability in S3D you can construct complex print jobs or do other things to create something other than air between layer 7 and the raft.
GCode below has only layers 7 and 8 for simplification:
-----------------------------------
First with .14mm separation.
; layer 7, Z = 2.2473
; tool H0.314 W0.400
; inner perimeter
; outer perimeter
G1 X17.182 Y17.199 F6000
G1 Z2.247 F600
G1 E1.0000 F1200
G1 X0.818 Y17.199 E0.8549 F3600
G1 X0.818 Y0.835 E0.8549
G1 X17.182 Y0.835 E0.8549
G1 X17.182 Y17.199 E0.8549
; layer 8, Z = 2.3073
; tool H0.200 W0.400
; inner perimeter
; outer perimeter
G1 X0.818 Y-0.835 F6000
G1 Z2.307 F600
G1 E1.0000 F1200
G1 X0.818 Y-17.199 E0.5443 F1800
G1 X17.182 Y-17.199 E0.5443
G1 X17.182 Y-0.835 E0.5443
G1 X0.818 Y-0.835 E0.5443
Next with 1mm separation.
; layer 7, Z = 3.1073
; tool H0.314 W0.400
; inner perimeter
; outer perimeter
G1 X17.182 Y17.199 F6000
G1 Z3.107 F600
G1 E1.0000 F1200
G1 X0.818 Y17.199 E0.8549 F3600
G1 X0.818 Y0.835 E0.8549
G1 X17.182 Y0.835 E0.8549
G1 X17.182 Y17.199 E0.8549
; layer 8, Z = 2.3073
; tool H0.200 W0.400
; inner perimeter
; outer perimeter
G1 X0.818 Y-0.835 F6000
G1 Z2.307 F600
G1 E1.0000 F1200
G1 X0.818 Y-17.199 E0.5443 F1800
G1 X17.182 Y-17.199 E0.5443
G1 X17.182 Y-0.835 E0.5443
G1 X0.818 Y-0.835 E0.5443